Showing : ChiPseeker • reset
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Cannot install packages in R/BiocManager_Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TR…
Bioconductor BioCManager ChIPseeker
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
7
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11
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6.7k
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annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 10.4 years ago by 25k • written 10.6 years ago by • 0
3
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10
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6.0k
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ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations in peaks from GRanges
chipseeker
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ▴ 50
1
vote
9
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5.4k
views
Question about ChiPseeker: plot other values in plotAvgProf2
ChiPseeker
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ▴ 50
2
votes
1
reply
5.2k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
6.5 years ago endrebak85 ▴ 40
0
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1
reply
4.5k
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ChIPseeker: Error in annotatePeak
Sequencing GO annotate ChIPseeker Sequencing GO annotate ChIPseeker
11.8 years ago António Miguel de Jesus Domingues ▴ 510
1
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2
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4.4k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
6.5 years ago researcher • 0
1
vote
11
replies
3.9k
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ChIPseeker question: provide custom csAnno to plots
chipseeker
10.3 years ago francesca casalino ▴ 50
0
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0
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3.8k
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How to define 'distal intergenic'
ChIPseeker
3.7 years ago Sanghoon • 0
2
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3
replies
3.8k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
8.3 years ago lifeng.liu.biology ▴ 10
2
votes
1
reply
3.8k
views
ChIPseeker mapping between keys and columns
chipseeker chipseq
updated 8.4 years ago by ▴ 690 • written 8.4 years ago by ▴ 60
3
votes
4
replies
3.8k
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ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
0
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2
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3.7k
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ChIPseeker annotatePeak definition
chipseeker
updated 9.5 years ago by ★ 1.2k • written 9.5 years ago by ▴ 140
0
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2
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3.7k
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custom annotation in annotatePeak
chipseeker Guangchuang Yu
8.1 years ago andrew.gehrke • 0
0
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1
reply
3.6k
views
error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
6.8 years ago Theo ▴ 10
1
vote
4
replies
3.5k
views
Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
5.0 years ago Kasit • 0
2
votes
6
replies
3.3k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
10.9 years ago • updated 10.8 years ago sarabusquets88 • 0
2
votes
2
replies
3.2k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
5.3 years ago • updated 5.1 years ago Mar Mar ▴ 20
5
votes
7
replies
3.2k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 60
0
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1
reply
3.2k
views
how to define the downstream range in ChIPseeker
ChIPseeker H3K27me3 chipseq chipseeker
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 10
1
vote
4
replies
3.1k
views
ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
chipseq chipseeker exon start site
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by • 0
5
votes
3
replies
3.1k
views
importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 10
0
votes
6
replies
3.0k
views
Chipseeker is unavabile on Linux CentOS7 ?
Bioconduct or Chipseeker CentOS7 Linux installation
updated 9.3 years ago by ★ 1.2k • written 9.3 years ago by • 0
0
votes
3
replies
3.0k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
8.1 years ago andrew.gehrke • 0
2
votes
1
reply
3.0k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
5.5 years ago amafon95 ▴ 20
0
votes
3
replies
2.9k
views
"input object should be a named list" error in ChIPseeker
ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot
updated 8.0 years ago by ★ 1.2k • written 8.0 years ago by • 0
3
votes
4
replies
2.8k
views
ChIPseeker::vennplot() fails with Error in ss[[1]] : subscript out of bounds
chipseeker venn vennplot genomicranges granges
9.7 years ago enricoferrero ▴ 680
0
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8
replies
2.7k
views
significance of ChIPseq peak overlap
chipseeker
updated 9.7 years ago by ★ 1.2k • written 9.7 years ago by ▴ 10
1
vote
1
reply
2.7k
views
Error: package or namespace load failed for 'ChIPseeker' in dyn.load(file, DLLpath = DLLpath
chipseeker
7.7 years ago liucz200904 • 0
3
votes
2
replies
2.6k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 7.0 years ago by ★ 2.1k • written 7.0 years ago by ▴ 100
0
votes
3
replies
2.5k
views
Chipseeker : problem running Chipseeker to ENCODE datasets
chipseeker
updated 10.8 years ago by ★ 1.2k • written 10.8 years ago by • 0
0
votes
1
reply
2.5k
views
ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
4.3 years ago william.ho • 0
0
votes
1
reply
2.5k
views
ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 4.9 years ago by ▴ 10 • written 4.9 years ago by ▴ 10
0
votes
1
reply
2.5k
views
ChIPseeker TSS plot
chipseeker plotAvgProf
updated 9.0 years ago by ★ 1.2k • written 9.1 years ago by • 0
1
vote
1
reply
2.4k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 4.6 years ago by • 0 • written 7.1 years ago by ▴ 10
0
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0
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2.4k
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Intergenic assigned to genes by ChIPseeker
chipseeker txdb.mmusculus.ucsc.mm10.knowngene
8.2 years ago doan.dinh • 0
0
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1
reply
2.4k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
3
votes
6
replies
2.4k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
7.6 years ago 94133 • 0
0
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1
reply
2.3k
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
5.9 years ago Assa Yeroslaviz ★ 1.5k
1
vote
3
replies
2.3k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by ▴ 10
0
votes
1
reply
2.2k
views
Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
6.4 years ago sutturka • 0
0
votes
1
reply
2.1k
views
ChIPseeker, read multiple peak files
chipseeker
updated 9.3 years ago by 68k • written 9.4 years ago by • 0
0
votes
1
reply
2.1k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 8.7 years ago by ★ 1.2k • written 8.7 years ago by • 0
0
votes
2
replies
2.0k
views
Annotation within ChIPSeeker mismatch geneId and annotation column
ChIPseeker
10.4 years ago n.kreim ▴ 20
1
vote
2
replies
2.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
3.0 years ago chavaleab • 0
3
votes
1
reply
2.0k
views
chipseeker annotation of focused genic regions
chipseeker annotatepeak
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by • 0
1
vote
3
replies
2.0k
views
ChIPseeker Error: Attempting to annotatePeaks
ChIPseeker software error
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by • 0
0
votes
1
reply
1.9k
views
ChIPseeker gene body plot
chipseeker visualization
updated 9.7 years ago by ★ 1.2k • written 9.7 years ago by ▴ 50
0
votes
1
reply
1.8k
views
ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
3.8 years ago Gyan Prakash Mishra ▴ 10
1
vote
3
replies
1.8k
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 20
97 results • Page 1 of 2
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Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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